[gmx-users] g_velacc

[David van der Spoel]

On 2011-05-27 14.39, Nilesh Dhumal wrote:
> How can I calculate the velocity autocorrelation function of a bond with
> Gromacs?
>
READ OUR ANSWERS.

> Nilesh
>
>
>
> On Fri, May 27, 2011 8:31 am, David van der Spoel wrote:
>> On 2011-05-27 14.26, Nilesh Dhumal wrote:
>>
>>> I am  calculating OH stretching frequency by fourier transform of
>>> velocity autocorrelation function.
>>>
>>> I could calculate the OH stretching frequnecy by calculating fourier
>>> transform of OH bond.
>>>
>>> I want to know how gromacs calculate the velocity autocorrelation
>>> function of a bond (If I define a bond in index file).
>>>
>>> Does is subtract the velocity of hydrogen from oxygen and then
>>> calculate the autocorrelation function?
>>>
>> No, see below! There is no tool that does exactly what you want, however
>> doing the velacc of just the hydrogen will come close.
>>> Nilesh
>>>
>>>
>>>
>>>
>>>
>>> On Fri, May 27, 2011 2:37 am, David van der Spoel wrote:
>>>
>>>> On 2011-05-26 22.48, Nilesh Dhumal wrote:
>>>>
>>>>
>>>>> Hello,
>>>>>
>>>>>
>>>>>
>>>>> I have calculated the velocity autocorrelation function of OH bond
>>>>> in glucose molecule. For this calculation I modified the index file.
>>>>> The
>>>>> modified part is pasted below.
>>>>>
>>>>> [ O10 ]
>>>>> 10   20
>>>>>
>>>>>
>>>>
>>>> where is the hydrogen? g_velacc knows nothing about bonds just atoms.
>>>>
>>>>
>>>>>
>>>>> 10 is oxygen no. and 20 is oxygen.
>>>>>
>>>>>
>>>>>
>>>>> I used following command to calculate the velocity autocorrelation
>>>>> function.
>>>>>
>>>>> g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o
>>>>>
>>>>>
>>>>> My question is how does the prog. calculate the velocity
>>>>> autocorrlation function.
>>>>>
>>>>> Does is subtract the velocity of hydrogen from oxygen and then
>>>>> calculate the autocorrelation function?
>>>>>
>>>>> I am using gromacs version 4.0.7.
>>>>>
>>>>>
>>>>>
>>>>> Thanks
>>>>>
>>>>>
>>>>>
>>>>> Nilesh
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Dept. of Cell&   Molec. Biol., Uppsala University.
>>>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
>>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se -- gmx-users mailing
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>>>>
>>>>
>>>
>>>
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell&  Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se --
>> gmx-users mailing list    gmx-users at gromacs.org
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>>
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se